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Genome-wide effects of Spt6 on RNA pol II and Histone H3 occupancy in budding yeast

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Saccharomyces cerevisiae

PROVIDER: GSE49928 | GEO | 2013/08/16

SECONDARY ACCESSION(S): PRJNA215349

REPOSITORIES: GEO

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Genome-wide effects of Spt6 on RNA pol II and Histone H3 occupancy in budding yeast

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2013-08-16 | E-GEOD-49928 | biostudies-arrayexpress

Genome-wide effects of Spt6 on RNA pol II and Histone H3 occupancy in budding yeast (ChIP-Chip)

Project description:whole genome analysis of RNA pol II and histone H3 in WT and Spt6-depleted cells using a tetracycline regulated ts degron mutant, spt6-td.

2013-08-16 | GSE49927 | GEO

Genome-wide effects of Spt6 on RNA pol II and Histone H3 occupancy in budding yeast (ChIP-Seq)

Project description:whole genome analysis of RNA pol II and histone H3 in WT and Spt6-depleted cells using a tetracycline regulated ts degron mutant, spt6-td.

2013-08-16 | GSE49926 | GEO

Genome-wide effects of Spt6 on RNA pol II and Histone H3 occupancy in budding yeast (ChIP-Seq)

Project description:whole genome analysis of RNA pol II and histone H3 in WT and Spt6-depleted cells using a tetracycline regulated ts degron mutant, spt6-td. ChIP-seq of histone H3and pol II in budding yeast (W303 background)

2013-08-16 | E-GEOD-49926 | biostudies-arrayexpress

Genome-wide effects of Spt6 on RNA pol II and Histone H3 occupancy in budding yeast (ChIP-Chip)

Project description:whole genome analysis of RNA pol II and histone H3 in WT and Spt6-depleted cells using a tetracycline regulated ts degron mutant, spt6-td. ChiP-ChIP using ligation-mediated PCR amplified material hybridized to Nimblegen 385K arrays 50mers median probe spacing 32 bp cat. No. C4214-00-01

2013-08-16 | E-GEOD-49927 | biostudies-arrayexpress

Genome-wide effects of Spt6 on RNA pol II and Histone H3 occupancy in budding yeast

Project description:Genome-wide effects of Spt6 on RNA pol II and Histone H3 occupancy in budding yeast

| PRJNA215349 | ENA

Histone H3 localizes to the centromeric DNA in budding yeast.

Project description:During cell division, segregation of sister chromatids to daughter cells is achieved by the poleward pulling force of microtubules, which attach to the chromatids by means of a multiprotein complex, the kinetochore. Kinetochores assemble at the centromeric DNA organized by specialized centromeric nucleosomes. In contrast to other eukaryotes, which typically have large repetitive centromeric regions, budding yeast CEN DNA is defined by a 125 bp sequence and assembles a single centromeric nucleosome. In budding yeast, as well as in other eukaryotes, the Cse4 histone variant (known in vertebrates as CENP-A) is believed to substitute for histone H3 at the centromeric nucleosome. However, the exact composition of the CEN nucleosome remains a subject of debate. We report the use of a novel ChIP approach to reveal the composition of the centromeric nucleosome and its localization on CEN DNA in budding yeast. Surprisingly, we observed a strong interaction of H3, as well as Cse4, H4, H2A, and H2B, but not histone chaperone Scm3 (HJURP in human) with the centromeric DNA. H3 localizes to centromeric DNA at all stages of the cell cycle. Using a sequential ChIP approach, we could demonstrate the co-occupancy of H3 and Cse4 at the CEN DNA. Our results favor a H3-Cse4 heterotypic octamer at the budding yeast centromere. Whether or not our model is correct, any future model will have to account for the stable association of histone H3 with the centromeric DNA.

| S-EPMC3364953 | biostudies-literature

Dominant effects of the histone mutant H3-L61R on Spt16-gene interactions in budding yeast.

Project description:Recent studies have unveiled an association between an L61R substitution within the human histone H3.3 protein and the presentation of neurodevelopmental disorders in two patients. In both cases, the mutation responsible for this substitution is encoded by one allele of the H3F3A gene and, if this mutation is indeed responsible for the disease phenotypes, it must act in a dominant fashion since the genomes of these patients also harbour three other alleles encoding wild-type histone H3.3. In our previous work in yeast, we have shown that most amino acid substitutions at H3-L61 cause an accumulation of the Spt16 component of the yFACT histone chaperone complex at the 3' end of transcribed genes, a defect we have attributed to impaired yFACT dissociation from chromatin following transcription. In those studies, however, the H3-L61R mutant had not been tested since it does not sustain viability when expressed as the sole source of histone H3 in cells. In the present work, we show that H3-L61R impairs proper Spt16 dissociation from genes when co-expressed with wild-type histone H3 in haploid cells as well as in diploid cells that express the mutant protein from one of four histone H3-encoding alleles. These results, combined with other studies linking loss of function mutations in human Spt16 and neurodevelopmental disorders, provide a possible molecular mechanism underlying the neurodevelopmental disorders seen in patients expressing the histone H3.3 L61R mutant.

| S-EPMC9665134 | biostudies-literature

Spt6 prevents transcription-coupled loss of posttranslationally modified histone H3.

Project description:The tail of histone H3 is an ideal medium for storing epigenetic information because displacement of histone H3 is heavily restricted during transcription. To maintain the locus-specific modifications of histone H3, histone molecules should be retained locally at the original position through multiple rounds of transcription. Here, we found that fission yeast Spt6, a highly conserved RNA polymerase II-interacting histone H3-H4 chaperone, is essential for the maintenance of Lys-4 and Lys-9 methylation of histone H3 in euchromatin and heterochromatin, respectively. In euchromatin, loss of Lys-4 methylated histone H3 and deposition of newly synthesized Lys-56 acetylated histone H3 induced by Spt6 inactivation were coupled with transcription. While in heterochromatin, Spt6 prevents histone turnover and cryptic transcription in parallel with Clr3 histone deacetylase. We propose that Spt6 retains posttranslationally modified histone H3 during transcription to maintain epigenome integrity.

| S-EPMC3711048 | biostudies-literature

The RSC complex localizes to coding sequences to regulate Pol II and histone occupancy.

Project description:ATP-dependent chromatin remodelers regulate chromatin structure during multiple stages of transcription. We report that RSC, an essential chromatin remodeler, is recruited to the open reading frames (ORFs) of actively transcribed genes genome wide, suggesting a role for RSC in regulating transcription elongation. Consistent with such a role, Pol II occupancy in the ORFs of weakly transcribed genes is drastically reduced upon depletion of the RSC catalytic subunit Sth1. RSC inactivation also reduced histone H3 occupancy across transcribed regions. Remarkably, the strongest effects on Pol II and H3 occupancy were confined to the genes displaying the greatest RSC ORF enrichment. Additionally, RSC recruitment to the ORF requires the activities of the SAGA and NuA4 HAT complexes and is aided by the activities of the Pol II CTD Ser2 kinases Bur1 and Ctk1. Overall, our findings strongly implicate ORF-associated RSC in governing Pol II function and in maintaining chromatin structure over transcribed regions.

| S-EPMC4258446 | biostudies-literature

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